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The crystal structure of the B. subtilis YphC GTPase in complex with GDP
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 290 0.2M sodium flouride, 20% (w/v) PEG3350, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.711 α = 90 b = 65.045 β = 90 c = 110.61 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MAR CCD 165 mm 2005-06-27 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SRS BEAMLINE PX10.1 0.9794, 0.9797, 1.0094 SRS PX10.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.5 30 99.9 0.098 17.8 6.8 16253 2 2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.5 2.65 99 0.32 5.1 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 2.5 19.96 15364 814 100 0.21815 0.21539 0.2505 0.27353 0.2867 RANDOM 41.463
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -2.29 -0.61 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.42 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 16.346 r_dihedral_angle_1_deg 12.283 r_scangle_it 2.644 r_scbond_it 1.863 r_mcbond_it 1.296 r_angle_refined_deg 1.251 r_mcangle_it 0.816 r_angle_other_deg 0.766
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.42 r_dihedral_angle_4_deg 19.1 r_dihedral_angle_3_deg 16.346 r_dihedral_angle_1_deg 12.283 r_scangle_it 2.644 r_scbond_it 1.863 r_mcbond_it 1.296 r_angle_refined_deg 1.251 r_mcangle_it 0.816 r_angle_other_deg 0.766 r_symmetry_vdw_other 0.249 r_nbd_refined 0.202 r_nbd_other 0.196 r_nbtor_refined 0.179 r_symmetry_hbond_refined 0.179 r_xyhbond_nbd_refined 0.143 r_symmetry_vdw_refined 0.093 r_metal_ion_refined 0.089 r_nbtor_other 0.083 r_chiral_restr 0.071 r_mcbond_other 0.062 r_bond_refined_d 0.01 r_bond_other_d 0.006 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3147 Nucleic Acid Atoms Solvent Atoms 31 Heterogen Atoms 57
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling SOLVE phasing